From 7a6cc3599a2c29809dbad5baa6da7d36eb82e929 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 16 Apr 2025 11:14:04 +0200
Subject: [PATCH] Just updated one or two small things
---
src/call.py | 3 +++
src/main.py | 14 +++++++-------
src/outils.py | 7 ++++++-
src/workflow.py | 4 +---
4 files changed, 17 insertions(+), 11 deletions(-)
diff --git a/src/call.py b/src/call.py
index bacbc20..be9135c 100644
--- a/src/call.py
+++ b/src/call.py
@@ -201,6 +201,9 @@ class Call(Executor):
raise Exception("This shouldn't happen")
return code.split()
+ def get_artificial_status(self):
+ return False
+
def analye_parameters(self, param):
#Step 1 -> get parameters
diff --git a/src/main.py b/src/main.py
index 426ba4d..4718360 100644
--- a/src/main.py
+++ b/src/main.py
@@ -19,13 +19,13 @@ class Main(Nextflow_Building_Blocks):
executors = self.get_all_executors_in_subworkflow()
pos = {}
for e in executors:
- code = e.get_code(get_OG = True)
- #We don't have to check the calls -> since there are renamed with their ids when we rewrite the code -> so it solve the issue
- if(code in seen and e.get_type()=="Operation"):
- raise BioFlowInsightError(f'Operation "{code}" appears twice in the workflow in the exact same way. BioFlow-Insight cannot rewrite the workflow then, try slighly changing how one of the executors is defined', type = "Rewrite Error")
- seen[code] = ''
- pos[e] = e.get_position_in_main(e)
- #TODO add sort here
+ if(not e.get_artificial_status()):
+ code = e.get_code(get_OG = True)
+ #We don't have to check the calls -> since there are renamed with their ids when we rewrite the code -> so it solve the issue
+ if(code in seen and e.get_type()=="Operation"):
+ raise BioFlowInsightError(f'Operation "{code}" appears twice in the workflow in the exact same way. BioFlow-Insight cannot rewrite the workflow then, try slighly changing how one of the executors is defined', type = "Rewrite Error")
+ seen[code] = e
+ pos[e] = e.get_position_in_main(e)
pos = {k: v for k, v in sorted(pos.items(), key=lambda item: item[1])}
for e in pos:
if(e.get_type()=="Call"):
diff --git a/src/outils.py b/src/outils.py
index 7116f09..fdc5535 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -1620,7 +1620,12 @@ def extract_tools(script, extract_general_tools = False):
tools.append("perl")
elif(extension==".jl"):
tools.append("julia")
- elif (ex!="" and len(ex)>1 and ex not in general_tools and ex[-1]!=":" and re.fullmatch(r"\w", ex[0])):
+ elif (ex!=""
+ and len(ex)>1
+ and ex not in general_tools
+ and ex[-1]!=":"
+ and re.fullmatch(r"\w", ex[0])
+ and "=" not in ex):
tools.append(ex)
#If the tool is java -> we search for the jar file in the command
if(ex=="java"):
diff --git a/src/workflow.py b/src/workflow.py
index 0d0abe0..ec9c12b 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -436,9 +436,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
for p in sampled:
name_select.append(p.get_alias())
return name_select
- else:
- print("here")
-
+
#This methods generates a random set of processes to consider as relavant
def generate_random_relevant_processes(self, alpha = -1):
--
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